I've never seen a game where at least one substitution was not made.
There are many reasons to replace a starter: pitchers get tired, batters aren't
hitting, players get injured, someone's ejected, or the manager makes a
strategic move. Whatever the reason, sooner or later you're going to
have to mark a substitution on your scorecard.

So, how do you do this? It depends on the substitution.

For batter substitutions, I draw a line between the last scorebox of the
previous batter and the first scorebox of the new batter.

Kitt pinch hits for Lawson

If the new batter is a pinch
hitter, place "PH" in the position box. If he is taking a
position in the field, use the normal position numbers. If players are
moved around in the field, you'll want to show that on your scorecard.
Usually, I make a note by the player's name indicating the
move.

When a substitution is made for the pitcher, place a
line under the score box of the last batter the previous pitcher faced.